4FOF

Crystal Structure of the blue-light absorbing form of the Thermosynechococcus elongatus PixJ GAF-domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.416 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Photo-Labile Thioether Linkage to Phycoviolobilin Provides the Foundation for the Blue/Green Photocycles in DXCF-Cyanobacteriochromes.

Burgie, E.S.Walker, J.M.Phillips, G.N.Vierstra, R.D.

(2013) Structure 21: 88-97

  • DOI: 10.1016/j.str.2012.11.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The phytochrome superfamily encompasses a diverse collection of photochromic photoreceptors in plants and microorganisms that employ a covalently linked bilin cradled in a cGMP-phosphodiesterase/adenylyl-cyclase/FhlA (GAF) domain to detect light. Whe ...

    The phytochrome superfamily encompasses a diverse collection of photochromic photoreceptors in plants and microorganisms that employ a covalently linked bilin cradled in a cGMP-phosphodiesterase/adenylyl-cyclase/FhlA (GAF) domain to detect light. Whereas most interconvert between red- and far-red-light-absorbing states, cyanobacteria also express variants called cyanobacteriochromes (CBCRs) that modify bilin absorption to collectively perceive the entire visible spectrum. Here, we present two X-ray crystallographic structures of the GAF domain from the blue/green photochromic CBCR PixJ from Thermosynechococcus elongatus. These structures confirm the hypothesis that CBCRs variably manipulate the chromophore π-conjugation system through isomerization and a second thioether linkage, in this case involving the bilin C10 carbon and Cys494 within a DXCF sequence characteristic of blue/green CBCRs. Biochemical studies support a mechanism for photoconversion whereby the second linkage ruptures on route to the green-light-absorbing state. Collectively, the TePixJ(GAF) models illustrate the remarkable structural and photochemical versatility among phytochromes and CBCRs in driving light perception.


    Organizational Affiliation

    Department of Biochemistry, 455 Babcock Drive, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: vierstra@wisc.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyl-accepting chemotaxis protein
A
171Thermosynechococcus elongatus (strain BP-1)Mutation(s): 1 
Find proteins for Q8DLC7 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DLC7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VRB
Query on VRB

Download SDF File 
Download CCD File 
A
Phycoviolobilin, blue light-absorbing form
3-[5-[(3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl)methyl]-2-[[5-[(Z)-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
C33 H42 N4 O6
KTSIPBCNIBDFRK-JTNIOKRPSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.416 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 104.232α = 90.00
b = 104.232β = 90.00
c = 115.314γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
RESOLVEphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references
  • Version 1.2: 2013-05-15
    Type: Non-polymer description
  • Version 1.3: 2017-11-15
    Type: Refinement description